Difference between revisions of "Bort"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=Bort parses Blast output and quantifies hits by contig and read counts. | |sw summary=Bort parses Blast output and quantifies hits by contig and read counts. | ||
| − | |bio domain=RNA-Seq | + | |sw logo=File:Image_for_Bort.jpeg |
| − | |bio tech=Any, | + | |bio domain=RNA-Seq quantification |
| − | |created by=Benjamin Rieger | + | |bio tech=Any, |
| + | |created by=Benjamin Rieger, Steffen Rapp, Hanno Schmidt | ||
|created at=Institute of Molecular Genetics, Biosafety Research and Consulting | |created at=Institute of Molecular Genetics, Biosafety Research and Consulting | ||
Johannes Gutenberg-University Mainz | Johannes Gutenberg-University Mainz | ||
Latest revision as of 16:50, 2 December 2015
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Application data |
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| Created by | Benjamin Rieger, Steffen Rapp, Hanno Schmidt |
|---|---|
| Biological application domain(s) | RNA-Seq quantification |
| Technology | Any |
| Created at | Institute of Molecular Genetics, Biosafety Research and Consulting
Johannes Gutenberg-University Mainz |
| Maintained? | Yes |
| Input format(s) | Standard Blast output |
| Output format(s) | Custom *.txt |
| Programming language(s) | Perl |
| Operating system(s) | any |
Summary: Bort parses Blast output and quantifies hits by contig and read counts.
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Description
Bort, the Blast Output Refinement Tool, has been written in Perl by Benjamin Rieger at the Institute of Molecular Genetics, Biosafety Research and Consulting at the Johannes Gutenberg-University in Mainz and is permanently getting extended and updated.
Bort's main function is to quantify transcript abundances of a NGS's library by their Blast annotation. Firstly, it parses extensive lists of Blast output and filters them e.g. by e-value to output a more concise overview for further processing. Hits can then be merged by accession number or description and quantified by contig and read count. Some functions are accessible only when using the SwissProt Database for Blastx searches, due to SissProt's high stringency in gene nomenclature. In principle, the quantification depends on counts obtained by overlap-layout-consensus assembly. However, mapping results against de Bruijn graph assemblies could be used easily with a few custom adjustments.
Links
none specified
References
To add a reference for Bort, enter the PubMed ID in the field below and click 'Add'.
Search for "Bort" in the SEQanswers forum / BioStar or:
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